Thread: Re: [apbs-users] APBS calculation for non protein molecules
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2011-12-10 15:49:14
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Hello – The development of implicit solvent radii and charges for non-protein molecules is a difficult task that requires a combination of quantum-derived charges and empirical radii parameterization. I am unaware of any radii parameters for the molecules you’ve mentioned. However, many have reported good results with the fairly portable Zap radii developed by Nicholls et al. together with AM1-BCC charges. I would encourage you to explore this parameterization scheme as a first step towards developing the charges and radii that you need. Good luck, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://nabaker.me From: raghu [mailto:rag...@gm...] Sent: Tuesday, December 06, 2011 6:22 PM To: apb...@go... Subject: [apbs-users] APBS calculation for non protein molecules Hi, I want to calculate charges for cellulose and chitin. Unfortunately I am at loss of how to use APBS for calculating charges for molecules such as Cellulose and Chitin, in general for non-protein molecules. Please let me know how should I proceed? Any hints/help is highly appreciated. Thanks in advance, Raghu |